Contacts of the helix formed by residues 116 - 128 (chain B) in PDB entry 4MXR
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLN 116 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B PHE* 3.4 32.6 - - + +
93B LEU* 3.6 12.8 - - + +
109B VAL* 3.1 28.7 + - - +
111B GLY* 3.5 11.0 + - - +
113B GLY 3.2 15.8 + - - +
114B ASN 2.9 0.4 - - - -
115B ASP* 1.3 79.7 - - - +
117B SER* 1.3 60.8 + - - +
119B PRO* 3.0 19.0 - - - +
120B ASN* 3.2 18.2 + - - +
270B ASP* 3.7 7.7 - - - +
271B MET 3.2 29.3 + - - +
272B SER* 2.7 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ASN* 2.8 34.5 + - - -
116B GLN* 1.3 76.6 - - - +
118B ALA* 1.3 59.7 + - - +
120B ASN* 3.8 2.7 - - - -
121B GLY 2.9 22.0 + - - -
157B PRO* 4.0 3.6 - - - -
158B PHE* 3.8 21.3 - - - -
161B LEU* 3.5 11.5 - - - +
224B PHE* 3.6 4.5 - - - -
226B SER* 3.2 7.2 + - - -
270B ASP* 2.8 24.3 + - - -
272B SER* 4.0 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B HIS* 6.2 1.1 - - + +
115B ASP 3.2 7.7 + - - +
116B GLN 3.2 0.2 - - - -
117B SER* 1.3 75.0 - - - +
119B PRO* 1.3 74.5 - - + +
121B GLY 3.2 1.6 + - - -
122B ARG* 3.0 34.3 + - - +
157B PRO* 4.0 14.5 - - + +
160B GLN* 3.6 39.3 - - + +
161B LEU* 3.5 10.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B HIS* 3.2 56.3 - - + +
93B LEU* 4.1 6.5 - - + -
94B GLU* 3.4 26.1 - - + +
115B ASP 3.1 12.1 - - - +
116B GLN 3.0 13.5 - - - +
118B ALA* 1.3 92.7 - - + +
120B ASN* 1.3 61.4 + - - +
122B ARG* 3.3 14.9 + - - +
123B ALA* 3.0 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B LEU* 3.4 13.4 - - - +
97B VAL* 3.3 22.7 - - - +
109B VAL* 3.9 10.7 - - - +
116B GLN* 3.2 20.4 + - - +
117B SER 3.8 0.7 - - - +
118B ALA 3.2 0.2 - - - -
119B PRO* 1.3 80.6 - - - +
121B GLY* 1.3 61.3 + - - +
123B ALA* 3.3 9.7 + - - +
124B MET* 3.2 24.9 + - - +
224B PHE* 3.7 19.5 - - + -
268B MET* 3.7 16.0 - - + +
270B ASP* 3.0 35.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B SER 2.9 18.3 + - - -
118B ALA 3.2 1.7 + - - -
120B ASN* 1.3 74.1 - - - +
122B ARG* 1.3 58.2 + - - +
124B MET* 3.2 7.7 + - - +
125B LEU* 2.9 31.3 + - - +
132B VAL* 5.4 0.3 - - - +
134B VAL* 5.7 2.7 - - - -
161B LEU* 3.7 21.1 - - - -
224B PHE* 3.9 12.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B HIS* 4.6 11.3 + - - +
94B GLU* 3.0 36.9 + - - +
118B ALA* 3.0 22.9 + - - +
119B PRO* 3.3 29.7 + - - +
121B GLY* 1.3 72.8 - - - +
123B ALA* 1.3 64.9 + - - +
125B LEU* 3.2 8.2 + - - +
126B ARG* 3.1 29.9 + - - +
160B GLN* 3.3 30.9 - - - +
161B LEU* 4.3 6.4 - - + +
164B GLU* 3.7 28.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B GLU* 3.4 29.1 - - - +
97B VAL* 3.6 22.9 - - + -
98B PHE* 3.6 18.5 - - - +
101B LEU* 3.8 2.8 - - - +
119B PRO 3.0 11.3 + - - +
120B ASN 3.4 10.3 - - - +
121B GLY 3.3 0.2 - - - -
122B ARG* 1.3 76.3 - - - +
124B MET* 1.3 57.1 + - - +
126B ARG* 3.4 1.7 + - - +
127B ALA* 3.0 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B LEU* 3.6 23.6 - - - -
120B ASN 3.2 16.4 + - - +
121B GLY* 3.2 9.4 + - - +
123B ALA* 1.3 77.2 - - - +
125B LEU* 1.3 57.2 + - - +
127B ALA* 3.1 1.2 + - - -
128B PHE* 2.9 48.8 + - + -
132B VAL* 3.3 21.3 - - + +
222B ASN 3.2 34.1 - - - +
223B THR 3.9 16.4 - - - +
224B PHE* 3.9 12.3 - - + +
267B MET* 4.0 4.5 - - + -
268B MET* 3.7 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B GLY 2.9 22.1 + - - +
122B ARG* 3.2 11.9 + - - +
124B MET* 1.3 75.0 - - - +
126B ARG* 1.3 62.7 + - + +
128B PHE 4.6 0.7 - - - +
129B PRO* 3.4 24.4 - - - +
130B GLY 4.4 2.6 + - - +
132B VAL* 3.8 29.8 - - + +
161B LEU* 4.6 5.8 - - + +
164B GLU* 3.5 42.4 - - + -
166B SER* 4.1 21.4 + - - +
167B PHE* 3.9 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B GLU* 3.1 44.5 + - - +
95B SER* 4.7 7.1 + - - +
98B PHE* 3.3 60.8 - - + +
122B ARG* 3.1 16.0 + - + +
123B ALA* 4.8 0.2 - - - +
125B LEU* 1.3 78.2 - - + +
127B ALA* 1.3 63.6 + - - +
128B PHE 3.3 0.2 - - - -
129B PRO* 3.7 14.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B PHE* 3.6 13.0 - - + -
101B LEU* 3.9 24.0 - - + -
102B ALA* 5.0 2.2 - - - +
123B ALA 3.0 18.0 + - - +
124B MET 3.1 3.8 + - - +
126B ARG* 1.3 79.6 - - - +
128B PHE* 1.3 85.2 + - + +
129B PRO* 3.6 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B LEU* 4.4 15.0 - - + -
124B MET* 2.9 43.6 + - + -
125B LEU 3.7 3.6 - - - +
127B ALA* 1.3 99.6 - - + +
129B PRO* 1.3 69.5 - - - +
130B GLY 3.2 0.7 + - - -
131B ASP* 3.0 14.7 + - + -
132B VAL* 3.5 15.7 - - + +
222B ASN* 3.3 44.0 - - + +
267B MET* 4.0 32.5 - - + -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il